Pack: Functional annotation of SNPs using next-generation text mining

Description:

Purpose:

This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology.

Result:

Concept Identifiers from the EMC ontology.

Comments:

Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example).

CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontology, GO:0008219. HG, HGNC, 4851. HMBD, Human Metabolome Database, HMDB01859. KEGD, KEGD, D00217. KEGG, KEGG, C12345. MESH, Medical Subject Headings, D000082. MGI, Mouse Genome Database, 96067. OM, OMIM, 143100. PUBC, PubChem Compound, 1983. PUBS, PubChem Substance, 7847284. RGD, Rat Genome Database, 68337. UG, UniGene, Mm.281700. UMLS, Unified Medical Language System, C0027439. UP, UniProt, P42858.

Description:

Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).

Description:

Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Description:

Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts.

Author comments:

Currently, PubMed is the underlying data source.

Description:

This workflow finds documents that serve as evidence for the association between two concepts.

Results:

Document titles Document identifiers

There seems to be a bug at the moment, since it returns empty values.

Description:

Purpose:

The workflow retrieves the concepts within a concept set.

The Web service/workflow currently returns no values (bug).

Description:

The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

Description:

Pupose:

The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Description:

Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles.

Result: A list of concepts ordered by their match to the query concept profiles.

Description:

Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles.

Result: A list of concepts ordered by their match to the query concept profiles.

Description:

Purpose:

Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding.

Author comments:

The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

Description:

Purpose:

The workflow maps a SNP (dbSNP id) to a gene (EntrezGene id).

Author comments:

The window for gene inclusion can be set using the set_width parameter. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.